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Cho C, Fei C, Jiang B, Yang W, Yuan HS. Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B. Protein Sci 2024; 33:e5131. [PMID: 39290110 PMCID: PMC11408749 DOI: 10.1002/pro.5131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/19/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024]
Abstract
DNA methyltransferase 3B (DNMT3B) plays a crucial role in DNA methylation during mammalian development. Mutations in DNMT3B are associated with human genetic diseases, particularly immunodeficiency, centromere instability, facial anomalies (ICF) syndrome. Although ICF syndrome-related missense mutations in the DNMT3B have been identified, their precise impact on protein structure and function remains inadequately explored. Here, we delve into the impact of four ICF syndrome-linked mutations situated in the DNMT3B dimeric interface (H814R, D817G, V818M, and R823G), revealing that each of these mutations compromises DNA-binding and methyltransferase activities to varying degrees. We further show that H814R, D817G, and V818M mutations severely disrupt the proper assembly of DNMT3B homodimer, whereas R823G does not. We also determined the first crystal structure of the methyltransferase domain of DNMT3B-DNMT3L tetrameric complex hosting the R823G mutation showing that the R823G mutant displays diminished hydrogen bonding interactions around T775, K777, G823, and Q827 in the protein-DNA interface, resulting in reduced DNA-binding affinity and a shift in sequence preference of +1 to +3 flanking positions. Altogether, our study uncovers a wide array of fundamental defects triggered by DNMT3B mutations, including the disassembly of DNMT3B dimers, reduced DNA-binding capacity, and alterations in flanking sequence preferences, leading to aberrant DNA hypomethylation and ICF syndrome.
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Affiliation(s)
- Chao‐Cheng Cho
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Cheng‐Yin Fei
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Bo‐Chen Jiang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Wei‐Zen Yang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Hanna S. Yuan
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Biochemistry and Molecular BiologyNational Taiwan UniversityTaipeiTaiwan, ROC
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2
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Wassing IE, Nishiyama A, Shikimachi R, Jia Q, Kikuchi A, Hiruta M, Sugimura K, Hong X, Chiba Y, Peng J, Jenness C, Nakanishi M, Zhao L, Arita K, Funabiki H. CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes. SCIENCE ADVANCES 2024; 10:eadp5753. [PMID: 39178260 PMCID: PMC11343034 DOI: 10.1126/sciadv.adp5753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/19/2024] [Indexed: 08/25/2024]
Abstract
Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency, centromeric instability, and facial anomalies syndrome, characterized by DNA hypomethylation at heterochromatin. It remains unclear why CDCA7-HELLS is the sole nucleosome remodeling complex whose deficiency abrogates the maintenance of DNA methylation. We here identify the unique zinc-finger domain of CDCA7 as an evolutionarily conserved hemimethylation-sensing zinc finger (HMZF) domain. Cryo-electron microscopy structural analysis of the CDCA7-nucleosome complex reveals that the HMZF domain can recognize hemimethylated CpG in the outward-facing DNA major groove within the nucleosome core particle, whereas UHRF1, the critical activator of the maintenance methyltransferase DNMT1, cannot. CDCA7 recruits HELLS to hemimethylated chromatin and facilitates UHRF1-mediated H3 ubiquitylation associated with replication-uncoupled maintenance DNA methylation. We propose that the CDCA7-HELLS nucleosome remodeling complex assists the maintenance of DNA methylation on chromatin by sensing hemimethylated CpG that is otherwise inaccessible to UHRF1 and DNMT1.
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Affiliation(s)
- Isabel E. Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
| | - Reia Shikimachi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Amika Kikuchi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Moeri Hiruta
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Keita Sugimura
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
| | - Xin Hong
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Christopher Jenness
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
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3
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León NY, Le TNU, Garvie A, Wong LH, Bagheri-Fam S, Harley VR. Y chromosome damage underlies testicular abnormalities in ATR-X syndrome. iScience 2024; 27:109629. [PMID: 38616920 PMCID: PMC11015497 DOI: 10.1016/j.isci.2024.109629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome features genital and testicular abnormalities including atypical genitalia and small testes with few seminiferous tubules. Our mouse model recapitulated the testicular defects when Atrx was deleted in Sertoli cells (ScAtrxKO) which displayed G2/M arrest and apoptosis. Here, we investigated the mechanisms underlying these defects. In control mice, Sertoli cells contain a single novel "GATA4 PML nuclear body (NB)" that contained the transcription factor GATA4, ATRX, DAXX, HP1α, and PH3 and co-localized with the Y chromosome short arm (Yp). ScAtrxKO mice contain single giant GATA4 PML-NBs with frequent DNA double-strand breaks (DSBs) in G2/M-arrested apoptotic Sertoli cells. HP1α and PH3 were absent from giant GATA4 PML-NBs indicating a failure in heterochromatin formation and chromosome condensation. Our data suggest that ATRX protects a Yp region from DNA damage, thereby preventing Sertoli cell death. We discuss Y chromosome damage/decondensation as a mechanism for testicular failure.
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Affiliation(s)
- Nayla Y. León
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Thanh Nha Uyen Le
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Andrew Garvie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lee H. Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Vincent R. Harley
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
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Unoki M. Exploring the intersection of epigenetics, DNA repair, and immunology from studies of ICF syndrome, an inborn error of immunity. Front Immunol 2024; 15:1405022. [PMID: 38799442 PMCID: PMC11116680 DOI: 10.3389/fimmu.2024.1405022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a rare autosomal recessive disorder, manifests with hypoglobulinemia and chromosomal instability accompanied by DNA hypomethylation. Pathological variants in the DNMT3B, ZBTB24, CDCA7, or HELLS genes underlie its etiology. Activated lymphocytes from patients often display distinctive multiradial chromosomes fused via pericentromeric regions. Recent studies have provided deeper insights into how pathological variants in ICF-related proteins cause DNA hypomethylation and chromosome instability. However, the understanding of the molecular pathogenesis underlying immunodeficiency is still in its nascent stages. In the past half-decade, the roles of CDCA7, HELLS, and ZBTB24 in classical non-homologous end joining during double-strand DNA break repair and immunoglobulin class-switch recombination (CSR) have been unveiled. Nevertheless, given the decreased all classes of immunoglobulins in most patients, CSR deficiency alone cannot fully account for the immunodeficiency. The latest finding showing dysregulation of immunoglobulin signaling may provide a clue to understanding the immunodeficiency mechanism. While less common, a subgroup of patients exhibits T-cell abnormalities alongside B-cell anomalies, including reduced regulatory T-cells and increased effector memory T- and follicular helper T-cells. The dysregulation of immunoglobulin signaling in B-cells, the imbalance in T-cell subsets, and/or satellite RNA-mediated activation of innate immune response potentially explain autoimmune manifestations in a subset of patients. These findings emphasize the pivotal roles of ICF-related proteins in both B- and T-cell functions. ICF syndrome studies have illuminated many fundamental mechanisms. Further investigations will certainly continue to unveil additional mechanisms and their interplay.
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Affiliation(s)
- Motoko Unoki
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Bilgic Eltan S, Nain E, Catak MC, Ezen E, Sefer AP, Karimi N, Kiykim A, Kolukisa B, Baser D, Bulutoglu A, Kasap N, Yorgun Altunbas M, Yalcin Gungoren E, Kendir Demirkol Y, Kutlug S, Hancioglu G, Dilek F, Yildiran A, Ozen A, Karakoc-Aydiner E, Erman B, Baris S. Evaluation of Clinical and Immunological Alterations Associated with ICF Syndrome. J Clin Immunol 2023; 44:26. [PMID: 38129713 DOI: 10.1007/s10875-023-01620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Immunodeficiency with centromeric instability and facial anomalies (ICF) syndrome is a rare autosomal recessive combined immunodeficiency. The detailed immune responses are not explored widely. We investigated known and novel immune alterations in lymphocyte subpopulations and their association with clinical symptoms in a well-defined ICF cohort. METHODS We recruited the clinical findings from twelve ICF1 and ICF2 patients. We performed detailed immunological evaluation, including lymphocyte subset analyses, upregulation, and proliferation of T cells. We also determined the frequency of circulating T follicular helper (cTFH) and regulatory T (Treg) cells and their subtypes by flow cytometry. RESULTS There were ten ICF1 and two ICF2 patients. We identified two novel homozygous missense mutations in the ZBTB24 gene. Respiratory tract infections were the most common recurrent infections among the patients. Gastrointestinal system (GIS) involvements were observed in seven patients. All patients received intravenous immunoglobulin replacement therapy and antibacterial prophylaxis; two died during the follow-up period. Immunologically, CD4+ T-cell counts, percentages of recent thymic emigrant T cells, and naive CD4+ T decreased in two, five, and four patients, respectively. Impaired T-cell proliferation and reduced CD25 upregulation were detected in all patients. These changes were more prominent in CD8+ T cells. GIS involvements negatively correlated with CD3+ T-, CD3+CD4+ T-, CD16+CD56+ NK-cell counts, and CD4+/CD8+ T-cell ratios. Further, we observed expanded cTFH cells and reduced Treg and follicular regulatory T cells with a skewing to a TH2-like phenotype in all tested subpopulations. CONCLUSION The ICF syndrome encompasses various manifestations affecting multiple end organs. Perturbed T-cell responses with increased cTFH and decreased Treg cells may provide further insight into the immune aberrations observed in ICF syndrome.
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Affiliation(s)
- Sevgi Bilgic Eltan
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ercan Nain
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Mehmet Cihangir Catak
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Asena Pınar Sefer
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nastaran Karimi
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayca Kiykim
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Burcu Kolukisa
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Dilek Baser
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Alper Bulutoglu
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nurhan Kasap
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Melek Yorgun Altunbas
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ezgi Yalcin Gungoren
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Yasemin Kendir Demirkol
- Division of Pediatric Genetics, Umraniye Education and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Seyhan Kutlug
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Gonca Hancioglu
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Fatih Dilek
- Department of Pediatrics, Faculty of Medicine, Atlas University, Istanbul, Turkey
| | - Alisan Yildiran
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Ahmet Ozen
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Safa Baris
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey.
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.
- Pediatric Allergy and Immunology, Marmara University Hospital, Istanbul, Turkey.
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Wassing IE, Nishiyama A, Hiruta M, Jia Q, Shikimachi R, Kikuchi A, Sugimura K, Hong X, Chiba Y, Peng J, Jenness C, Nakanishi M, Zhao L, Arita K, Funabiki H. CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572350. [PMID: 38187757 PMCID: PMC10769307 DOI: 10.1101/2023.12.19.572350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, characterized by hypomethylation at heterochromatin. The unique zinc-finger domain, zf-4CXXC_R1, of CDCA7 is widely conserved across eukaryotes but is absent from species that lack HELLS and DNA methyltransferases, implying its specialized relation with methylated DNA. Here we demonstrate that zf-4CXXC_R1 acts as a hemimethylated DNA sensor. The zf-4CXXC_R1 domain of CDCA7 selectively binds to DNA with a hemimethylated CpG, but not unmethylated or fully methylated CpG, and ICF disease mutations eliminated this binding. CDCA7 and HELLS interact via their N-terminal alpha helices, through which HELLS is recruited to hemimethylated DNA. While placement of a hemimethylated CpG within the nucleosome core particle can hinder its recognition by CDCA7, cryo-EM structure analysis of the CDCA7-nucleosome complex suggests that zf-4CXXC_R1 recognizes a hemimethylated CpG in the major groove at linker DNA. Our study provides insights into how the CDCA7-HELLS nucleosome remodeling complex uniquely assists maintenance DNA methylation.
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Affiliation(s)
- Isabel E. Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639 Japan
| | - Moeri Hiruta
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Reia Shikimachi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Amika Kikuchi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Keita Sugimura
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639 Japan
| | - Xin Hong
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639 Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639 Japan
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Christopher Jenness
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639 Japan
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
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Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
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Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
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8
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Scelfo A, Fachinetti D. Centromere: A Trojan horse for genome stability. DNA Repair (Amst) 2023; 130:103569. [PMID: 37708591 DOI: 10.1016/j.dnarep.2023.103569] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Centromeres play a key role in the maintenance of genome stability to prevent carcinogenesis and diseases. They are specialized chromosome loci essential to ensure faithful transmission of genomic information across cell generations by mediating the interaction with spindle microtubules. Nonetheless, while fulfilling these essential roles, their distinct repetitive composition and susceptibility to mechanical stresses during cell division render them susceptible to breakage events. In this review, we delve into the present understanding of the underlying causes of centromere fragility, from the mechanisms governing its DNA replication and repair, to the pathways acting to counteract potential challenges. We propose that the centromere represents a "Trojan horse" exerting vital functions that, at the same time, potentially threatens whole genome stability.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
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9
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Berner J, van de Wetering C, Jimenez Heredia R, Rashkova C, Ferdinandusse S, Koster J, Weiss JG, Frohne A, Giuliani S, Waterham HR, Castanon I, Brunner J, Boztug K. Phosphomevalonate kinase deficiency expands the genetic spectrum of systemic autoinflammatory diseases. J Allergy Clin Immunol 2023; 152:1025-1031.e2. [PMID: 37364720 PMCID: PMC10549927 DOI: 10.1016/j.jaci.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND In the isoprenoid biosynthesis pathway, mevalonate is phosphorylated in 2 subsequent enzyme steps by MVK and PMVK to generate mevalonate pyrophosphate that is further metabolized to produce sterol and nonsterol isoprenoids. Biallelic pathogenic variants in MVK result in the autoinflammatory metabolic disorder MVK deficiency. So far, however, no patients with proven PMVK deficiency due to biallelic pathogenic variants in PMVK have been reported. OBJECTIVES This study reports the first patient with functionally confirmed PMVK deficiency, including the clinical, biochemical, and immunological consequences of a homozygous missense variant in PMVK. METHODS The investigators performed whole-exome sequencing and functional studies in cells from a patient who, on clinical and immunological evaluation, was suspected of an autoinflammatory disease. RESULTS The investigators identified a homozygous PMVK p.Val131Ala (NM_006556.4: c.392T>C) missense variant in the index patient. Pathogenicity was supported by genetic algorithms and modeling analysis and confirmed in patient cells that revealed markedly reduced PMVK enzyme activity due to a virtually complete absence of PMVK protein. Clinically, the patient showed various similarities as well as distinct features compared to patients with MVK deficiency and responded well to therapeutic IL-1 inhibition. CONCLUSIONS This study reported the first patient with proven PMVK deficiency due to a homozygous missense variant in PMVK, leading to an autoinflammatory disease. PMVK deficiency expands the genetic spectrum of systemic autoinflammatory diseases, characterized by recurrent fevers, arthritis, and cytopenia and thus should be included in the differential diagnosis and genetic testing for systemic autoinflammatory diseases.
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Affiliation(s)
- Jakob Berner
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; Department of Dermatology, Venereology and Allergology, Klinik Landstraße, Vienna, Austria
| | - Cheryl van de Wetering
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raul Jimenez Heredia
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Vienna, Austria
| | - Christina Rashkova
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; Medical University of Vienna, Vienna, Austria
| | - Sacha Ferdinandusse
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - Janet Koster
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - Johannes G Weiss
- Department of Pediatrics, Medical University Innsbruck, Innsbruck, Austria; Institute of Developmental Immunology, Medical University Innsbruck, Innsbruck, Austria
| | - Alexandra Frohne
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sarah Giuliani
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Hans R Waterham
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - Irinka Castanon
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Jürgen Brunner
- Department of Pediatrics, Medical University Innsbruck, Innsbruck, Austria; Faculty of Medicine and Dentistry, Danube Private University, Krems, Austria
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Vienna, Austria.
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10
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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. eLife 2023; 12:RP86721. [PMID: 37769127 PMCID: PMC10538959 DOI: 10.7554/elife.86721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Isabel E Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
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11
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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526367. [PMID: 36778482 PMCID: PMC9915587 DOI: 10.1101/2023.01.30.526367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Isabel E. Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065
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12
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Martinez-Delgado B, Barrero MJ. Epigenomic Approaches for the Diagnosis of Rare Diseases. EPIGENOMES 2022; 6:21. [PMID: 35997367 PMCID: PMC9397041 DOI: 10.3390/epigenomes6030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the disease. Patients with negative results for these tests frequently undergo whole exome or genome sequencing, leading to the identification of the molecular cause of the disease in 50% of patients at best. Therefore, a significant proportion of patients remain undiagnosed after sequencing their genome. Recently, approaches based on functional aspects of the genome, including transcriptomics and epigenomics, are beginning to emerge. Here, we will review these approaches, including studies that have successfully provided diagnoses for complex undiagnosed cases.
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Affiliation(s)
- Beatriz Martinez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER U758, 28029 Madrid, Spain
| | - Maria J. Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
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13
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Qin W, Brands X, van’t Veer C, de Vos AF, Scicluna BP, van der Poll T. DNA Methyltransferase 3b in Myeloid Cells Does Not Affect the Acute Immune Response in the Airways during Pseudomonas Pneumonia. Cells 2022; 11:787. [PMID: 35269409 PMCID: PMC8909799 DOI: 10.3390/cells11050787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
DNA methyltransferase 3b (Dnmt3b) has been suggested to play a role in the host immune response during bacterial infection. Neutrophils and other myeloid cells are crucial for lung defense against Pseudomonas (P.) aeruginosa infection. This study aimed to investigate the role of Dnmt3b in neutrophils and myeloid cells during acute pneumonia caused by P. aeruginosa. Neutrophil-specific (Dnmt3bfl/flMrp8Cre) or myeloid cell-specific (Dnmt3bfl/flLysMCre) Dnmt3b-deficient mice and littermate control mice were infected with P. aeruginosa PAK via the airways. Bacteria burdens, neutrophil recruitment, and activation (CD11b expression, myeloperoxidase, and elastase levels), interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF) were measured in bronchoalveolar lavage fluid (BALF) at 6 and 24 h after infection. Our data showed that the bacterial loads and neutrophil recruitment and activation did not differ in BALF obtained from neutrophil-specific Dnmt3b-deficient and control mice, whilst BALF IL-6 and TNF levels were lower in the former group at 24 but not at 6 h after infection. None of the host response parameters measured differed between myeloid cell-specific Dnmt3b-deficient and control mice. In conclusion, dnmt3b deficiency in neutrophils or myeloid cells does not affect acute immune responses in the airways during Pseudomonas pneumonia.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
| | - Xanthe Brands
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
| | - Cornelis van’t Veer
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
| | - Alex F. de Vos
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
| | - Brendon P. Scicluna
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Tom van der Poll
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.B.); (C.v.V.); (A.F.d.V.); (B.P.S.); (T.v.d.P.)
- Division of Infectious Diseases, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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14
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Fang M, Su Z, Abolhassani H, Zhang W, Jiang C, Cheng B, Luo L, Wu J, Wang S, Lin L, Wang X, Wang L, Aghamohammadi A, Li T, Zhang X, Hammarström L, Liu X. T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects. J Clin Immunol 2022; 42:375-393. [PMID: 34825286 PMCID: PMC8821531 DOI: 10.1007/s10875-021-01178-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Both DNA damage response and methylation play a crucial role in antigen receptor recombination by creating a diverse repertoire in developing lymphocytes, but how their defects relate to T cell repertoire and phenotypic heterogeneity of immunodeficiency remains obscure. We studied the TCR repertoire in patients with the mutation in different genes (ATM, DNMT3B, ZBTB24, RAG1, DCLRE1C, and JAK3) and uncovered distinct characteristics of repertoire diversity. We propose that early aberrancies in thymus T cell development predispose to the heterogeneous phenotypes of the immunodeficiency spectrum. Shorter CDR3 lengths in ATM-deficient patients, resulting from a decreased number of nucleotide insertions during VDJ recombination in the pre-selected TCR repertoire, as well as the increment of CDR3 tyrosine residues, lead to the enrichment of pathology-associated TCRs, which may contribute to the phenotypes of ATM deficiency. Furthermore, patients with DNMT3B and ZBTB24 mutations who exhibit discrepant phenotypes present longer CDR3 lengths and reduced number of known pathology-associated TCRs.
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Affiliation(s)
- Mingyan Fang
- BGI-Shenzhen, Shenzhen, 518083, China
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - Zheng Su
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Hassan Abolhassani
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | | | | | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Liya Lin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tao Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, 518083, China.
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
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15
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Unoki M. Chromatin remodeling in replication-uncoupled maintenance DNA methylation and chromosome stability: Insights from ICF syndrome studies. Genes Cells 2021; 26:349-359. [PMID: 33960584 PMCID: PMC9292322 DOI: 10.1111/gtc.12850] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022]
Abstract
Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is characterized by frequent appearance of multiradial chromosomes, which are distinctive chromosome fusions that occur at hypomethylated pericentromeric regions comprising repetitive sequences, in activated lymphocytes. The syndrome is caused by mutations in DNMT3B, ZBTB24, CDCA7, or HELLS. De novo DNA methylation is likely defective in patients with ICF syndrome harboring mutations in DNMT3B, whereas accumulating evidence suggests that replication‐uncoupled maintenance DNA methylation of late‐replicating regions is impaired in patients with ICF syndrome harboring mutations in ZBTB24, CDCA7, or HELLS. ZBTB24 is a transcriptional activator of CDCA7, and CDCA7 and HELLS compose a chromatin remodeling complex and are involved in the maintenance DNA methylation through an interaction with UHRF1 in a feed‐forward manner. Furthermore, our recent studies possibly provided the missing link between DNA hypomethylation and the formation of the abnormal chromosomes; it could occur via aberrant transcription from the hypomethylated regions, followed by pathological R‐loop formation. The homologous‐recombination dominant condition caused by a defect in nonhomologous end joining observed in several types of ICF syndrome could facilitate the formation of multiradial chromosomes. Here, the latest knowledge regarding maintenance DNA methylation and chromosome stability provided by those studies is reviewed.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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16
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Kiaee F, Zaki-Dizaji M, Hafezi N, Almasi-Hashiani A, Hamedifar H, Sabzevari A, Shirkani A, Zian Z, Jadidi-Niaragh F, Aghamahdi F, Goudarzvand M, Yazdani R, Abolhassani H, Aghamohammadi A, Azizi G. Clinical, Immunologic and Molecular Spectrum of Patients with Immunodeficiency, Centromeric Instability, and Facial Anomalies (ICF) Syndrome: A Systematic Review. Endocr Metab Immune Disord Drug Targets 2021; 21:664-672. [PMID: 32533820 DOI: 10.2174/1871530320666200613204426] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Immunodeficiency, centromeric instability and facial dysmorphism (ICF) syndrome is a rare autosomal recessive immune disorder presenting with hypogammaglobulinemia, developmental delay, and facial anomalies. The ICF type 1, type 2, type 3 and type 4 are characterized by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS gene, respectively. This study aimed to present a comprehensive description of the clinical, immunologic and genetic features of patients with ICF syndrome. METHODS PubMed, Web of Science, and Scopus were searched systemically to find eligible studies. RESULTS Forty-eight studies with 118 ICF patients who met the inclusion criteria were included in our study. Among these patients, 60% reported with ICF-1, 30% with ICF-2, 4% with ICF-3, and 6% with ICF-4. The four most common symptoms reported in patients with ICF syndrome were: delay in motor development, low birth weight, chronic infections, and diarrhea. Intellectual disability and preterm birth among patients with ICF-2 and failure to thrive, sepsis and fungal infections among patients with ICF-1 were also more frequent. Moreover, the median levels of all three immunoglobulins (IgA, IgG, IgM) were markedly reduced within four types of ICF syndrome. CONCLUSION The frequency of diagnosed patients with ICF syndrome has increased. Early diagnosis of ICF is important since immunoglobulin supplementation or allogeneic stem cell transplantation can improve the disease-free survival rate.
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Affiliation(s)
- Fatemeh Kiaee
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Nasim Hafezi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amir Almasi-Hashiani
- Department of Epidemiology, School of Health, Arak University of Medical Sciences, Arak, Iran
| | - Haleh Hamedifar
- CinnaGen Medical Biotechnology Research Center, Alborz University of medical sciences, Karaj, Iran
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of medical sciences, Karaj, Iran
| | - Afshin Shirkani
- Allergy and clinical Immunology Department, School of Medicine, Bushehr University of Medical Science, Bushehr, Iran
| | - Zeineb Zian
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | | | - Fatemeh Aghamahdi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdi Goudarzvand
- Department of Physiology and Pharmacology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
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17
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Parodi C, Di Fede E, Peron A, Viganò I, Grazioli P, Castiglioni S, Finnell RH, Gervasini C, Vignoli A, Massa V. Chromatin Imbalance as the Vertex Between Fetal Valproate Syndrome and Chromatinopathies. Front Cell Dev Biol 2021; 9:654467. [PMID: 33959609 PMCID: PMC8093873 DOI: 10.3389/fcell.2021.654467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Prenatal exposure to valproate (VPA), an antiepileptic drug, has been associated with fetal valproate spectrum disorders (FVSD), a clinical condition including congenital malformations, developmental delay, intellectual disability as well as autism spectrum disorder, together with a distinctive facial appearance. VPA is a known inhibitor of histone deacetylase which regulates the chromatin state. Interestingly, perturbations of this epigenetic balance are associated with chromatinopathies, a heterogeneous group of Mendelian disorders arising from mutations in components of the epigenetic machinery. Patients affected from these disorders display a plethora of clinical signs, mainly neurological deficits and intellectual disability, together with distinctive craniofacial dysmorphisms. Remarkably, critically examining the phenotype of FVSD and chromatinopathies, they shared several overlapping features that can be observed despite the different etiologies of these disorders, suggesting the possible existence of a common perturbed mechanism(s) during embryonic development.
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Affiliation(s)
- Chiara Parodi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Di Fede
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Angela Peron
- Human Pathology and Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy.,Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, San Paolo Hospital, ASST Santi Paolo e Carlo, Università degli Studi di Milano, Milan, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Ilaria Viganò
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Castiglioni
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Richard H Finnell
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics and Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Cristina Gervasini
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Aglaia Vignoli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
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18
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Mihìc P, Hédouin S, Francastel C. Centromeres Transcription and Transcripts for Better and for Worse. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:169-201. [PMID: 34386876 DOI: 10.1007/978-3-030-74889-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Centromeres are chromosomal regions that are essential for the faithful transmission of genetic material through each cell division. They represent the chromosomal platform on which assembles a protein complex, the kinetochore, which mediates attachment to the mitotic spindle. In most organisms, centromeres assemble on large arrays of tandem satellite repeats, although their DNA sequences and organization are highly divergent among species. It has become evident that centromeres are not defined by underlying DNA sequences, but are instead epigenetically defined by the deposition of the centromere-specific histone H3 variant, CENP-A. In addition, and although long regarded as silent chromosomal loci, centromeres are in fact transcriptionally competent in most species, yet at low levels in normal somatic cells, but where the resulting transcripts participate in centromere architecture, identity, and function. In this chapter, we discuss the various roles proposed for centromere transcription and their transcripts, and the potential molecular mechanisms involved. We also discuss pathological cases in which unscheduled transcription of centromeric repeats or aberrant accumulation of their transcripts are pathological signatures of chromosomal instability diseases. In sum, tight regulation of centromeric satellite repeats transcription is critical for healthy development and tissue homeostasis, and thus prevents the emergence of disease states.
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Affiliation(s)
- Pia Mihìc
- Université De Paris, Epigenetics and Cell Fate, CNRS UMR7216, Paris, France
| | - Sabrine Hédouin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire Francastel
- Université De Paris, Epigenetics and Cell Fate, CNRS UMR7216, Paris, France.
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19
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Metabolic Regulation of Epigenetic Modifications and Cell Differentiation in Cancer. Cancers (Basel) 2020; 12:cancers12123788. [PMID: 33339101 PMCID: PMC7765496 DOI: 10.3390/cancers12123788] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Cancer cells change their metabolism to support a chaotic and uncontrolled growth. In addition to meeting the metabolic needs of the cell, these changes in metabolism also affect the patterns of gene activation, changing the identity of cancer cells. As a consequence, cancer cells become more aggressive and more resistant to treatments. In this article, we present a review of the literature on the interactions between metabolism and cell identity, and we explore the mechanisms by which metabolic changes affect gene regulation. This is important because recent therapies under active investigation target both metabolism and gene regulation. The interactions of these new therapies with existing chemotherapies are not known and need to be investigated. Abstract Metabolic reprogramming is a hallmark of cancer, with consistent rewiring of glucose, glutamine, and mitochondrial metabolism. While these metabolic alterations are adequate to meet the metabolic needs of cell growth and proliferation, the changes in critical metabolites have also consequences for the regulation of the cell differentiation state. Cancer evolution is characterized by progression towards a poorly differentiated, stem-like phenotype, and epigenetic modulation of the chromatin structure is an important prerequisite for the maintenance of an undifferentiated state by repression of lineage-specific genes. Epigenetic modifiers depend on intermediates of cellular metabolism both as substrates and as co-factors. Therefore, the metabolic reprogramming that occurs in cancer likely plays an important role in the process of the de-differentiation characteristic of the neoplastic process. Here, we review the epigenetic consequences of metabolic reprogramming in cancer, with particular focus on the role of mitochondrial intermediates and hypoxia in the regulation of cellular de-differentiation. We also discuss therapeutic implications.
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20
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Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:ijms21218062. [PMID: 33137955 PMCID: PMC7662960 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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21
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Unoki M, Sharif J, Saito Y, Velasco G, Francastel C, Koseki H, Sasaki H. CDCA7 and HELLS suppress DNA:RNA hybrid-associated DNA damage at pericentromeric repeats. Sci Rep 2020; 10:17865. [PMID: 33082427 PMCID: PMC7576824 DOI: 10.1038/s41598-020-74636-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
Immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome is a rare autosomal recessive disorder that is caused by mutations in either DNMT3B, ZBTB24, CDCA7, HELLS, or yet unidentified gene(s). Previously, we reported that the CDCA7/HELLS chromatin remodeling complex facilitates non-homologous end-joining. Here, we show that the same complex is required for the accumulation of proteins on nascent DNA, including the DNMT1/UHRF1 maintenance DNA methylation complex as well as proteins involved in the resolution or prevention of R-loops composed of DNA:RNA hybrids and ssDNA. Consistent with the hypomethylation state of pericentromeric repeats, the transcription and formation of aberrant DNA:RNA hybrids at the repeats were increased in ICF mutant cells. Furthermore, the ectopic expression of RNASEH1 reduced the accumulation of DNA damage at a broad range of genomic regions including pericentromeric repeats in these cells. Hence, we propose that hypomethylation due to inefficient DNMT1/UHRF1 recruitment at pericentromeric repeats by defects in the CDCA7/HELLS complex could induce pericentromeric instability, which may explain a part of the molecular pathogenesis of ICF syndrome.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan.
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, 411-8540, Japan
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan
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22
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Current genetic landscape in common variable immune deficiency. Blood 2020; 135:656-667. [PMID: 31942606 DOI: 10.1182/blood.2019000929] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/14/2019] [Indexed: 12/14/2022] Open
Abstract
Using whole-exome sequencing to examine the genetic causes of immune deficiency in 235 common variable immunodeficiency (CVID) patients seen in the United States (Mount Sinai, New York), 128 patients from Sweden, and 208 from Iran revealed 68 known disease-causing genes underlying this heterogeneous immune defect. The patients at the time of study ranged from 4 to 90 years of age. Overall, 31%, 36%, and 54% of the patients in the US, Swedish, or Iranian cohorts had mutations. The multiplicity of genes identified in the 571 subjects reflects the complex requirements of B-cell antigen signaling, activation, survival, migration, maturation, and maintenance of antibody-secreting memory B-cell populations to the plasma cell stage. For the US and Swedish cohorts, CVID subjects with noninfectious complications, lymphoid infiltrations, inflamatory conditions, or autoimmunity were somewhat more likely to have an identifiable gene, but in both cohorts, numerous subjects with these medical conditions had no potential gene that could be assigned. Specific clinical patterns of illnesses were also not linked to any given gene defect as there was considerable overlap in clinical presentations. These observations led to a new perspective on the complexity of the immunologic phenotype found in CVID syndrome.
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23
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DNA methylation in satellite repeats disorders. Essays Biochem 2020; 63:757-771. [PMID: 31387943 DOI: 10.1042/ebc20190028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
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24
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Human subtelomeric DNA methylation: regulation and roles in telomere function. Curr Opin Genet Dev 2020; 60:9-16. [PMID: 32109830 DOI: 10.1016/j.gde.2020.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Subtelomeres are the regions at chromosome ends, immediately adjacent to the terminal telomeric repeats. The majority of human subtelomeres are CpG-rich in their distal two kilobases, and are methylated during early embryonic development by the de novo DNA methyltransferase DNMT3B. The biological relevance of subtelomeric DNA methylation is highlighted by the presence of promoters for the long non-coding TERRA transcripts in these CpG-rich regions. Indeed, deviant subtelomeric methylation has been linked with abnormal telomeric phenotypes, as most strikingly found in ICF syndrome. Here we review recent studies that explore new aspects of subtelomeric methylation regulation and demonstrate the significance of maintaining proper DNA methylation at the extreme distal human subtelomeric regions.
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25
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Aktar S, Sasaki H, Unoki M. Identification of ZBTB24 protein domains and motifs for heterochromatin localization and transcriptional activation. Genes Cells 2019; 24:746-755. [PMID: 31561277 DOI: 10.1111/gtc.12723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022]
Abstract
Immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome is a rare autosomal recessive disorder caused by mutations in either DNMT3B, ZBTB24, CDCA7, HELLS or an unknown gene(s). Among the known causative genes, ZBTB24 encodes a member of the BTB-zinc finger (ZF) transcription factor family. The protein possesses a BTB domain, an AT-hook and eight C2H2 ZF motifs. All ZBTB24 mutations reported in ICF patients are predicted to disrupt at least one ZF motif. Here, we show that both AT-hook and distinct ZF motifs, particularly the 6th motif, of human and mouse ZBTB24 proteins are important for their heterochromatin localization. On the other hand, the 6th and 7th ZF motifs, and not the AT-hook or the BTB domain, of the human and mouse proteins are essential for transcriptional activation of CDCA7, another ICF causative gene and a known target of ZBTB24. By deletion analysis of the human CDCA7 promoter, we show that two motifs for ZBTB24 binding are important for transcriptional activation of this gene. These results reveal the evolutionarily conserved domains and motifs important for the biological function of ZBTB24, which provides a basis for understanding the molecular mechanisms underlying the pathogenesis of ICF syndrome.
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Affiliation(s)
- Sharmin Aktar
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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26
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Hu H, Chen C, Shi S, Li B, Duan S. The gene mutations and subtelomeric DNA methylation in immunodeficiency, centromeric instability and facial anomalies syndrome. Autoimmunity 2019; 52:192-198. [PMID: 31476899 DOI: 10.1080/08916934.2019.1657846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disorder, which is characteristic of a severe impairment of immunity. In the genetic aspect, ICF is featured with mutations primarily located in the specific genes (DNMT3B for ICF1, ZBTB24 for ICF2, CDCA7 for ICF3, and HELLS for ICF4). The subtelomeric region is defined as 500 kb at the terminal of each autosomal arm. And subtelomeric DNA fragments can partially regulate key biological activities, including chromosome movement and localization in the nucleus. In this review, we updated and summarized gene mutations in ICF based on the previous review. In addition, we focused on the correlation between subtelomeric DNA methylation and ICF. The relationship between subtelomeric methylation and telomere length in ICF was also summarized.
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Affiliation(s)
- Haochang Hu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Chujia Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shanping Shi
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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27
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Scelfo A, Fachinetti D. Keeping the Centromere under Control: A Promising Role for DNA Methylation. Cells 2019; 8:cells8080912. [PMID: 31426433 PMCID: PMC6721688 DOI: 10.3390/cells8080912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 01/22/2023] Open
Abstract
In order to maintain cell and organism homeostasis, the genetic material has to be faithfully and equally inherited through cell divisions while preserving its integrity. Centromeres play an essential task in this process; they are special sites on chromosomes where kinetochores form on repetitive DNA sequences to enable accurate chromosome segregation. Recent evidence suggests that centromeric DNA sequences, and epigenetic regulation of centromeres, have important roles in centromere physiology. In particular, DNA methylation is abundant at the centromere, and aberrant DNA methylation, observed in certain tumors, has been correlated to aneuploidy and genomic instability. In this review, we evaluate past and current insights on the relationship between centromere function and the DNA methylation pattern of its underlying sequences.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
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28
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DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell 2019; 71:882-895. [PMID: 30241605 DOI: 10.1016/j.molcel.2018.08.008] [Citation(s) in RCA: 329] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.
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29
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Velasco G, Francastel C. Genetics meets DNA methylation in rare diseases. Clin Genet 2018; 95:210-220. [DOI: 10.1111/cge.13480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Guillaume Velasco
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
| | - Claire Francastel
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
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30
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Unoki M, Funabiki H, Velasco G, Francastel C, Sasaki H. CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome. J Clin Invest 2018; 129:78-92. [PMID: 30307408 DOI: 10.1172/jci99751] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in CDCA7 and HELLS that respectively encode a CXXC-type zinc finger protein and an SNF2 family chromatin remodeler cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome types 3 and 4. Here, we demonstrate that the classical nonhomologous end joining (C-NHEJ) proteins Ku80 and Ku70, as well as HELLS, coimmunoprecipitated with CDCA7. The coimmunoprecipitation of the repair proteins was sensitive to nuclease treatment and an ICF3 mutation in CDCA7 that impairs its chromatin binding. The functional importance of these interactions was strongly suggested by the compromised C-NHEJ activity and significant delay in Ku80 accumulation at DNA damage sites in CDCA7- and HELLS-deficient HEK293 cells. Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. Although less prominent, cells with mutations in the other ICF genes DNMT3B and ZBTB24 (responsible for ICF types 1 and 2, respectively) showed similar defects. Importantly, lymphoblastoid cells from ICF patients shared the same changes detected in the mutant HEK293 cells to varying degrees. Although the C-NHEJ defect alone did not cause CG hypomethylation, CDCA7 and HELLS are involved in maintaining CG methylation at centromeric and pericentromeric repeats. The defect in C-NHEJ may account for some common features of ICF cells, including centromeric instability, abnormal chromosome segregation, and apoptosis.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York, USA
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Thompson JJ, Kaur R, Sosa CP, Lee JH, Kashiwagi K, Zhou D, Robertson KD. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation. Nucleic Acids Res 2018; 46:10034-10051. [PMID: 30085123 PMCID: PMC6212772 DOI: 10.1093/nar/gky682] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in gene expression, is being increasingly appreciated. ZBTB24, a poorly characterized zinc-finger protein, or the de novo methyltransferase DNMT3B, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting an underlying mechanistic link. Chromatin immunoprecipitation coupled with loss-of-function approaches in model systems revealed common loci bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function. We identify a ZBTB24 DNA binding motif, which is contained within the promoters of most of its transcriptional targets, including CDCA7, AXIN2, and OSTC. Direct binding of ZBTB24 at the promoters of these genes targets them for transcriptional activation. ZBTB24 binding at the promoters of RNF169 and CAMKMT, however, targets them for transcriptional repression. The involvement of ZBTB24 targets in diverse cellular programs, including the VDR/RXR and interferon regulatory pathways, suggest that ZBTB24's role as a transcriptional regulator is not restricted to immune cells.
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Affiliation(s)
- Joyce J Thompson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Rupinder Kaur
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Carlos P Sosa
- Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Stabile12-58, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Katsunobu Kashiwagi
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Dan Zhou
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
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32
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Kamae C, Imai K, Kato T, Okano T, Honma K, Nakagawa N, Yeh TW, Noguchi E, Ohara A, Shigemura T, Takahashi H, Takakura S, Hayashi M, Honma A, Watanabe S, Shigemori T, Ohara O, Sasaki H, Kubota T, Morio T, Kanegane H, Nonoyama S. Clinical and Immunological Characterization of ICF Syndrome in Japan. J Clin Immunol 2018; 38:927-937. [PMID: 30353301 DOI: 10.1007/s10875-018-0559-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is a rare autosomal recessive primary immunodeficiency. Hypogammaglobulinemia is a major manifestation of ICF syndrome, but immunoglobulin replacement therapy does not seem to be effective for some ICF patients. Therefore, we aimed to reassess the immunological characteristics of this syndrome. METHODS Eleven Japanese patients with ICF syndrome were enrolled. We performed whole-exome sequencing in four cases and homozygosity mapping using SNP analysis in two. We evaluated their clinical manifestations and immunological status. RESULTS We newly diagnosed six ICF patients who had tentatively been diagnosed with common variable immunodeficiency. We identified two novel mutations in the DNMT3B gene and one novel mutation in the ZBTB24 gene. All patients showed low serum IgG and/or IgG2 levels and were treated by periodic immunoglobulin replacement therapy. Three of the six patients showed worse results of the mitogen-induced lymphocyte proliferation test. Analyses of lymphocyte subpopulations revealed that CD19+CD27+ memory B cells were low in seven of nine patients, CD3+ T cells were low in three patients, CD4/8 ratio was inverted in five patients, CD31+ recent thymic emigrant cells were low in two patients, and CD19+ B cells were low in four patients compared with those in the normal controls. ICF2 patients showed lower proportions of CD19+ B cells and CD16+56+ NK cells and significantly higher proportions of CD3+ T cells than ICF1 patients. T cell receptor excision circles were undetectable in two patients. Despite being treated by immunoglobulin replacement therapy, three patients died of influenza virus, fatal viral infection with persistent Epstein-Barr virus infection, or JC virus infection. One of three dead patients showed normal intelligence with mild facial anomaly. Two patients presented with autoimmune or inflammatory manifestations. Infectious episodes decreased in three patients who were started on trimethoprim-sulfamethoxazole and/or antifungal drugs in addition to immunoglobulin replacement therapy. These patients might have suffered from T cell immunodeficiency. CONCLUSION These results indicate that patients with ICF syndrome have a phenotype of combined immunodeficiency. Thus, to achieve a better prognosis, these patients should be treated as having combined immunodeficiency in addition to receiving immunoglobulin replacement therapy.
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Affiliation(s)
- Chikako Kamae
- Department of Pediatrics, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama, 359-0042, Japan.
- Department of Pediatrics, Self Defense Forces Central Hospital, Tokyo, Japan.
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tamaki Kato
- Department of Pediatrics, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama, 359-0042, Japan
- Department of Pediatrics, Self Defense Forces Central Hospital, Tokyo, Japan
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kenichi Honma
- Department of Pediatrics, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama, 359-0042, Japan
| | - Noriko Nakagawa
- Department of Pediatrics, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama, 359-0042, Japan
- Department of Pediatrics, Self Defense Forces Central Hospital, Tokyo, Japan
| | - Tzu-Wen Yeh
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University School of Medicine, Tokyo, Japan
| | - Tomonari Shigemura
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hiroshi Takahashi
- Department of Neurology, National Hospital Organization, Tottori Medical Center, Tottori, Japan
| | - Shunichi Takakura
- Department of Infectious Diseases, Okinawa Chubu Hospital, Uruma, Japan
| | | | - Aoi Honma
- Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Seiichi Watanabe
- Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Tomoko Shigemori
- Department of Pediatrics, Nippon Medical School Tama Nagayama Hospital, Tama, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeo Kubota
- Faculty of Child Studies, Seitoku University, Matsudo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama, 359-0042, Japan
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Toubiana S, Velasco G, Chityat A, Kaindl AM, Hershtig N, Tzur-Gilat A, Francastel C, Selig S. Subtelomeric methylation distinguishes between subtypes of Immunodeficiency, Centromeric instability and Facial anomalies syndrome. Hum Mol Genet 2018; 27:3568-3581. [PMID: 30010917 DOI: 10.1093/hmg/ddy265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Human telomeres and adjacent subtelomeres are packaged as heterochromatin. Subtelomeric DNA undergoes methylation during development by DNA methyltransferase 3B (DNMT3B), including the CpG-rich promoters of the long non-coding RNA (TERRA) embedded in these regions. The factors that direct DNMT3B methylation to human subtelomeres and maintain this methylation throughout lifetime are yet unknown. The importance of subtelomeric methylation is manifested through the abnormal telomeric phenotype in Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome type 1 patients carrying mutations in DNMT3B. Patient cells demonstrate subtelomeric hypomethylation, accompanied by elevated TERRA transcription, accelerated telomere shortening and premature senescence of fibroblasts. ICF syndrome can arise due to mutations in at least three additional genes, ZBTB24 (ICF2), CDCA7 (ICF3) and HELLS (ICF4). While pericentromeric repeat hypomethylation is evident in all ICF syndrome subtypes, the status of subtelomeric DNA methylation had not been described for patients of subtypes 2-4. Here we explored the telomeric phenotype in cells derived from ICF2-4 patients with the aim to determine whether ZBTB24, CDCA7 and HELLS also play a role in establishing and/or maintaining human subtelomeric methylation. We found normal subtelomeric methylation in ICF2-4 and accordingly low TERRA levels and unperturbed telomere length. Moreover, depleting the ICF2-4-related proteins in normal fibroblasts did not influence subtelomeric methylation. Thus, these gene products are not involved in establishing or maintaining subtelomeric methylation. Our findings indicate that human subtelomeric heterochromatin has specialized methylation regulation and highlight the telomeric phenotype as a characteristic that distinguishes ICF1 from ICF2-4.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Guillaume Velasco
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Adi Chityat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Center for Chronically Sick Children, Institute of Cell Biology and Neurobiology, Augustenburger Platz 1, Berlin, Germany
| | | | - Aya Tzur-Gilat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
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Bronkhorst AJ, Wentzel JF, Ungerer V, Peters DL, Aucamp J, de Villiers EP, Holdenrieder S, Pretorius PJ. Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells. Tumour Biol 2018; 40:1010428318801190. [PMID: 30261820 DOI: 10.1177/1010428318801190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The true importance of cell-free DNA in human biology, together with the potential scale of its clinical utility, is tarnished by a lack of understanding of its composition and origin. In investigating the cell-free DNA present in the growth medium of cultured 143B cells, we previously demonstrated that the majority of cell-free DNA is neither a product of apoptosis nor necrosis. In the present study, we investigated the composition and origin of this cell-free DNA population using next-generation sequencing. We found that the cell-free DNA comprises mainly of repetitive DNA, including α-satellite DNA, mini satellites, and transposons that are currently active or exhibit the capacity to become reactivated. A significant portion of these cell-free DNA fragments originates from specific chromosomes, especially chromosomes 1 and 9. In healthy adult somatic cells, the centromeric and pericentromeric regions of these chromosomes are normally densely methylated. However, in many cancer types, these regions are preferentially hypomethylated. This can lead to double-stranded DNA breaks or it can directly impair the formation of proper kinetochore structures. This type of chromosomal instability is a precursor to the formation of nuclear anomalies, including lagging chromosomes and anaphase bridges. DNA fragments derived from these structures can recruit their own nuclear envelope and form secondary nuclear structures known as micronuclei, which can localize to the nuclear periphery and bud out from the membrane. We postulate that the majority of cell-free DNA present in the growth medium of cultured 143B cells originates from these micronuclei.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Johannes F Wentzel
- 2 Centre of Excellence for Nutrition (CEN), North-West University, Potchefstroom, South Africa
| | - Vida Ungerer
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Dimetrie L Peters
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
| | - Janine Aucamp
- 4 Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | | | - Stefan Holdenrieder
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Piet J Pretorius
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
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Jenness C, Giunta S, Müller MM, Kimura H, Muir TW, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A 2018; 115:E876-E885. [PMID: 29339483 PMCID: PMC5798369 DOI: 10.1073/pnas.1717509115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations in CDCA7, the SNF2 family protein HELLS (LSH), or the DNA methyltransferase DNMT3b cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. While it has been speculated that DNA methylation defects cause this disease, little is known about the molecular function of CDCA7 and its functional relationship to HELLS and DNMT3b. Systematic analysis of how the cell cycle, H3K9 methylation, and the mitotic kinase Aurora B affect proteomic profiles of chromatin in Xenopus egg extracts revealed that HELLS and CDCA7 form a stoichiometric complex on chromatin, in a manner sensitive to Aurora B. Although HELLS alone fails to remodel nucleosomes, we demonstrate that the HELLS-CDCA7 complex possesses nucleosome remodeling activity. Furthermore, CDCA7 is essential for loading HELLS onto chromatin, and CDCA7 harboring patient ICF mutations fails to recruit the complex to chromatin. Together, our study identifies a unique bipartite nucleosome remodeling complex where the functional remodeling activity is split between two proteins and thus delineates the defective pathway in ICF syndrome.
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Affiliation(s)
- Christopher Jenness
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Manuel M Müller
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065;
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CHAVOSHZADEH Z, HASHEMITARI A, DAROUGAR S. Neurological Manifestations of Primary Immunodeficiencies. IRANIAN JOURNAL OF CHILD NEUROLOGY 2018; 12:7-23. [PMID: 30026765 PMCID: PMC6045935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Primary immunodeficiencies (PID) are a heterogeneous group of disorders with a variable clinical spectrum of manifestations. The central nervous system may be involved in PID with symptoms which may present initially or develop at later stages. The purpose of this study was to review the neurological manifestations of different PID syndromes. MATERIALS & METHODS We focused on 104 selected studies on PID with certain neurological abnormalities which may accompany these disorders or may later signify a PID in their course. RESULTS Diverse neurological deficits accompanying certain PIDs may be mild or they may greatly influence the course of the disease with major impacts on the quality of life of these patients. CONCLUSION Early recognition and treatment is important to prevent or reduce future irreversible neurological sequelae. Therefore physicians should be aware of the neurological features accompanying PID.
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Affiliation(s)
- Zahra CHAVOSHZADEH
- Department of Immunology and Allergy, Mofid’s Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sepideh DAROUGAR
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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37
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Patients with a Kabuki syndrome phenotype demonstrate DNA methylation abnormalities. Eur J Hum Genet 2017; 25:1335-1344. [PMID: 29255178 DOI: 10.1038/s41431-017-0023-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/05/2023] Open
Abstract
Kabuki syndrome is a monogenic disorder caused by loss of function variants in either of two genes encoding histone-modifying enzymes. We performed targeted sequencing in a cohort of 27 probands with a clinical diagnosis of Kabuki syndrome. Of these, 12 had causative variants in the two known Kabuki syndrome genes. In 2, we identified presumptive loss of function de novo variants in KMT2A (missense and splice site variants), a gene that encodes another histone modifying enzyme previously exclusively associated with Wiedermann-Steiner syndrome. Although Kabuki syndrome is a disorder of histone modification, we also find alterations in DNA methylation among individuals with a Kabuki syndrome diagnosis relative to matched normal controls, regardless of whether they carry a variant in KMT2A or KMT2D or not. Furthermore, we observed characteristic global abnormalities of DNA methylation that distinguished patients with a loss of function variant in KMT2D or missense or splice site variants in either KMT2D or KMT2A from normal controls. Our results provide new insights into the relationship of genotype to epigenotype and phenotype and indicate cross-talk between histone and DNA methylation machineries exposed by inborn errors of the epigenetic apparatus.
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38
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Sagie S, Edni O, Weinberg J, Toubiana S, Kozlovski T, Frostig T, Katzin N, Bar-Am I, Selig S. Non-random length distribution of individual telomeres in immunodeficiency, centromeric instability and facial anomalies syndrome, type I. Hum Mol Genet 2017; 26:4244-4256. [PMID: 28973513 DOI: 10.1093/hmg/ddx313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in the de novo DNA methyltransferase DNMT3B lead to Immunodeficiency, Centromeric Instability and Facial anomalies (ICF) syndrome, type I. This syndrome is characterized, among other hypomethylated genomic loci, by severe subtelomeric hypomethylation that is associated with abnormally short telomere length. While it was demonstrated that the mean telomere length is significantly shorter in ICF type I cells, it is unknown whether all telomeres are equally vulnerable to shortening. To study this question we determined by combined telomere-FISH and spectral karyotyping the relative length of each individual telomere in lymphoblastoid cell lines (LCLs) generated from multiple ICF syndrome patients and control individuals. Here we confirm the short telomere lengths, and demonstrate that telomere length variance in the ICF patient group is much larger than in the control group, suggesting that not all telomeres shorten in a uniform manner. We identified a subgroup of telomeres whose relatively short lengths can distinguish with a high degree of certainty between a control and an ICF metaphase, proposing that in ICF syndrome cells, certain individual telomeres are consistently at greater risk to shorten than others. The majority of these telomeres display high sequence identity at the distal 2 kb of their subtelomeres, suggesting that the attenuation in DNMT3B methylation capacity affects individual telomeres to different degrees based, at least in part, on the adjacent subtelomeric sequence composition.
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Omer Edni
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Joseph Weinberg
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Tal Kozlovski
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Tzviel Frostig
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Nirit Katzin
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Irit Bar-Am
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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39
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Lyko F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat Rev Genet 2017; 19:81-92. [PMID: 29033456 DOI: 10.1038/nrg.2017.80] [Citation(s) in RCA: 830] [Impact Index Per Article: 118.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA methyltransferase (DNMT) family comprises a conserved set of DNA-modifying enzymes that have a central role in epigenetic gene regulation. Recent studies have shown that the functions of the canonical DNMT enzymes - DNMT1, DNMT3A and DNMT3B - go beyond their traditional roles of establishing and maintaining DNA methylation patterns. This Review analyses how molecular interactions and changes in gene copy numbers modulate the activity of DNMTs in diverse gene regulatory functions, including transcriptional silencing, transcriptional activation and post-transcriptional regulation by DNMT2-dependent tRNA methylation. This mechanistic diversity enables the DNMT family to function as a versatile toolkit for epigenetic regulation.
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Affiliation(s)
- Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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40
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Moura CMD, Bastos PR, Ribeiro JSV, Ribeiro MG, Amorim MR, Costa-Lima MA. DNA (cytosine-5)-methyltransferase 3B ( DNMT 3B) polymorphism and risk of Down syndrome offspring. Saudi J Biol Sci 2017; 25:101-104. [PMID: 29379364 PMCID: PMC5775107 DOI: 10.1016/j.sjbs.2017.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022] Open
Abstract
Down syndrome (DS) is the most common form of human genetic mental retardation. Several polymorphisms in genes coding folic acid cycle enzymes have been associated to the risk of bearing a DS child; however, the results are controversial. S-adenosyl-l-methionine (SAM) is an important intermediate of folic acid pathway and acts as methyl donor and substrate for DNA (cytosine-5)-methyltransferase 3B (DNMT3B – EC 2.1.1.37) de novo methylation processes during embryogenesis. Recent studies suggest that a functional polymorphism of DNMT 3B in maternal genotype may be associated with a decreased risk of having a DS child. We herein investigate the association of this polymorphism with the occurrence of DS in a Brazilian population. We have genotyped 111 mothers of DS infants (MDS) and 212 control mothers (CM) through PCR-RFLP. The observed genotypic frequencies were CC = 0.22; CT = 0.49 and TT = 0.29 in CM, and CC = 0.30; CT = 0.52 and TT = 0.18 in MDS. Allelic frequencies were C = 0.47 and T = 0.53 in CM and C = 0.56 and T = 0.44 in MDS. No deviation of HWE was observed, and both DNMT 3B rs2424913 genotype (χ2 = 4.53; DF = 1; P = 0.03) and allelic (χ2 = 4.90; DF = 1; P = 0.03) frequencies show significant differences between MDS and CM. The presence of the mutant DNMT 3B T allele decreases 30% the risk of bearing a DS child (OR = 0.69; 95% CI: 0.50–0.96; P = 0.03), and the risk is diminished up to 45% in association with the homozygous genotype (OR = 0.54; 95% CI: 0.31–0.96; P = 0.04). Our results suggest that women harboring the single nucleotide polymorphism DNMT 3B rs2424913 have a decreased risk of a DS pregnancy, and further studies are necessary to confirm this protective effect.
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Affiliation(s)
- Cláudia Melo de Moura
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Brazil
| | - Pedro Ribeiro Bastos
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Brazil
| | - Julyana S V Ribeiro
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Brazil
| | - Márcia Gonçalves Ribeiro
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brazil
| | - Márcia Rodrigues Amorim
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Brazil.,Programa de Pós Graduação em Neurologia, Universidade Federal Fluminense, Brazil
| | - Marcelo Aguiar Costa-Lima
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Brazil
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Singh P, Sailu S, Palchamy E, Coumar MS, Baluchamy S. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 2017; 34:145. [PMID: 28730333 DOI: 10.1007/s12032-017-1008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022]
Abstract
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.
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Affiliation(s)
- Prachi Singh
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sarvagalla Sailu
- Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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42
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Gössling KL, Schipp C, Fischer U, Babor F, Koch G, Schuster FR, Dietzel-Dahmen J, Wieczorek D, Borkhardt A, Meisel R, Kuhlen M. Hematopoietic Stem Cell Transplantation in an Infant with Immunodeficiency, Centromeric Instability, and Facial Anomaly Syndrome. Front Immunol 2017; 8:773. [PMID: 28713390 PMCID: PMC5491950 DOI: 10.3389/fimmu.2017.00773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022] Open
Abstract
Immunodeficiency, centromeric instability, and facial anomaly (ICF) syndrome is a rare autosomal recessive genetic condition with severe immunodeficiency, which leads to lethal infections if not recognized and treated in early childhood. Up-to-date treatment regimens consist of prophylactic and supportive treatment of the recurrent infections. Here, we report the case of a 1-year-old boy of Moroccan consanguineous parents, who was diagnosed at 4 months of age with ICF syndrome with a homozygous missense mutation in the DNMT3B gene. He was initially admitted to the hospital with recurrent pulmonary infections from the opportunistic pathogen Pneumocystis jirovecii (PJ). Further immunological workup revealed agammaglobulinemia in the presence of B cells. After successful recovery from the PJ pneumonia, he underwent hematopoietic stem cell transplantation (HSCT) from the HLA-matched healthy sister using a chemotherapeutic conditioning regimen consisting of treosulfan, fludarabine, and thiotepa. Other than acute chemotherapy-associated side effects, no serious adverse events occurred. Six months after HSCT immune-reconstitution, he had a stable chimerism with 2.9% autologous portion in the peripheral blood and a normal differential blood cell count, including all immunoglobulin subtypes. This is one of the first cases of successful HSCT in ICF syndrome. Early diagnosis and subsequent HSCT can prevent severe opportunistic infections and cure the immunodeficiency. Centromeric instability and facial anomaly remain unaffected. Although the long-term patient outcome and the neurological development remain to be seen, this curative therapy for immunodeficiency improves life expectancy and quality of life. This case is meant to raise physicians awareness for ICF syndrome and highlight the consideration for HSCT in ICF syndrome early on.
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Affiliation(s)
- Katharina L Gössling
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Cyrill Schipp
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Ute Fischer
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Florian Babor
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Gerhard Koch
- Department of Pediatrics, Allgemeines Krankenhaus Hagen, Hagen, Germany
| | - Friedhelm R Schuster
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Jutta Dietzel-Dahmen
- Medical Faculty, Department of Human Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Medical Faculty, Department of Human Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Arndt Borkhardt
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Roland Meisel
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
| | - Michaela Kuhlen
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Düsseldorf, Düsseldorf, Germany
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43
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Chen CC, Mellone BG. Chromatin assembly: Journey to the CENter of the chromosome. J Cell Biol 2017; 214:13-24. [PMID: 27377247 PMCID: PMC4932374 DOI: 10.1083/jcb.201605005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/14/2016] [Indexed: 11/22/2022] Open
Abstract
All eukaryotic genomes are packaged into basic units of DNA wrapped around histone proteins called nucleosomes. The ability of histones to specify a variety of epigenetic states at defined chromatin domains is essential for cell survival. The most distinctive type of chromatin is found at centromeres, which are marked by the centromere-specific histone H3 variant CENP-A. Many of the factors that regulate CENP-A chromatin have been identified; however, our understanding of the mechanisms of centromeric nucleosome assembly, maintenance, and reorganization remains limited. This review discusses recent insights into these processes and draws parallels between centromeric and noncentromeric chromatin assembly mechanisms.
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Affiliation(s)
- Chin-Chi Chen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
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Abstract
Activation of oncogenes or the deactivation of tumor suppressor genes has long been established as the fundamental mechanism leading towards carcinogenesis. Although this age old axiom is vastly accurate, thorough study over the last 15years has given us unprecedented information on the involvement of epigenetic in cancer. Various biochemical pathways that are essential towards tumorigenesis are regulated by the epigenetic phenomenons like remodeling of nucleosome by histone modifications, DNA methylation and miRNA mediated targeting of various genes. Moreover the presence of mutations in the genes controlling the epigenetic players has further strengthened the association of epigenetics in cancer. This merger has opened up newer avenues for targeted anti-cancer drug therapy with numerous pharmaceutical industries focusing on expanding their research and development pipeline with epigenetic drugs. The information provided here elaborates the elementary phenomena of the various epigenetic regulators and discusses their alteration associated with the development of cancer. We also highlight the recent developments in epigenetic drugs combining preclinical and clinical data to signify this evolving field in cancer research.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India.
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Rechavi E, Lev A, Eyal E, Barel O, Kol N, Barhom SF, Pode-Shakked B, Anikster Y, Somech R, Simon AJ. A Novel Mutation in a Critical Region for the Methyl Donor Binding in DNMT3B Causes Immunodeficiency, Centromeric Instability, and Facial Anomalies Syndrome (ICF). J Clin Immunol 2016; 36:801-809. [PMID: 27734333 DOI: 10.1007/s10875-016-0340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is an extremely rare autosomal recessive disease. The immune phenotype is characterized by hypogammaglobulinemia in the presence of B cells. T cell lymphopenia also develops in some patients. We sought to further investigate the immune defect in an ICF patient with a novel missense mutation in DNMT3B and a severe phenotype. METHODS Patient lymphocytes were examined for subset counts, immunoglobulin levels, T and B cell de novo production (via excision circles) and receptor repertoire diversity. Mutated DNMT3B protein structure was modeled to assess the effect of a mutation located outside of the catalytic region on protein function. RESULTS A novel homozygous missense mutation, Ala585Thr, was found in DNMT3B. The patient had decreased B cell counts with hypogammaglobulinemia, and normal T cell counts. CD4+ T cells decreased over time, leading to an inversion of the CD4+ to CD8+ ratio. Excision circle copy numbers were normal, signifying normal de novo lymphocyte production, but the ratio between naïve and total B cells was low, indicating decreased in vivo B cell replication. T and B cell receptor repertoires displayed normal diversity. Computerized modeling of the mutated Ala585 residue suggested reduced thermostability, possibly affecting the enzyme kinetics. CONCLUSIONS Our results highlight the existence of a T cell defect that develops over time in ICF patient, in addition to the known B cell dysfunction. With intravenous immunoglobulin (IVIG) treatment ameliorating the B cell defect, the extent of CD4+ lymphopenia may determine the severity of ICF immunodeficiency.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Eran Eyal
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Barel
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Nitzan Kol
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Sarit Farage Barhom
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Metabolic Disease Unit, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
| | - Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Institute of Hematology, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
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Plourde KV, Labrie Y, Ouellette G, Pouliot MC, Durocher F. Genome-wide methylation analysis of DNMT3B gene isoforms revealed specific methylation profiles in breast cell lines. Epigenomics 2016; 8:1209-26. [PMID: 27586997 DOI: 10.2217/epi-2016-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM The goal of this study is to characterize the specific methylation profile triggered by DNMT3B protein isoforms expressed at different levels in breast cell lines. MATERIALS & METHODS Microarray DNA methylation data were analyzed and associated with functional genome annotation data. RESULTS A large spectrum of DNMT3B3/DNMT3B2 expression ratio values was observed in parental breast cell lines. According to their methylation profiles, hierarchical clustering of untransfected cell lines revealed clustering based on their ER/PR status. Overexpression of DNMT3B3 triggered methylation changes of thousands of CpG sites in breast cells. Based on the trend of methylation changes, the results suggest an antiproliferative action of the DNMT3B3 isoform through a dominant negative effect on its wild-type counterpart DNMT3B2. CONCLUSION This study revealed specific pathways modulated by DNMT3B isoforms, which could regulate cell proliferation and other biological mechanisms. This illustrates the importance of multiple interactions between isoforms in the complexity of methylation processes.
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Affiliation(s)
- Karine V Plourde
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Yvan Labrie
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Geneviève Ouellette
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Marie-Christine Pouliot
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Francine Durocher
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
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Downregulation of ZBTB24 hampers the G0/1- to S-phase cell-cycle transition via upregulating the expression of IRF-4 in human B cells. Genes Immun 2016; 17:276-82. [PMID: 27098601 DOI: 10.1038/gene.2016.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 12/27/2022]
Abstract
It has been recently identified that loss-of-function mutations in the uncharacterized gene ZBTB24 (zinc finger and BTB domain-containing 24) cause ICF2 (immunodeficiency, centromeric instability and facial anomalies syndrome 2) with immunological characteristics of greatly reduced serum antibodies and circulating memory B cells. ZBTB24 belongs to the large ZBTB family of transcriptional repressors with members like B-cell lymphoma 6 (BCL-6; ZBTB27) playing critical roles in B-cell functions. Given the genotype-phenotype correlation analyses in ICF2 patients and the high expression of ZBTB24 in human B cells, we, in the present study, investigated the function of ZBTB24 in human B-cell line Raji cells. Knockdown of endogenous ZBTB24 by small hairpin RNAs results in a significantly reduced proliferation through blocking the G0/1- to S-phase cell-cycle progression, but not apoptosis induction. Moreover, downregulation of ZBTB24 increases the expression of IRF-4 (interferon regulatory factor 4) and Blimp-1 (B lymphocyte-induced maturation protein 1), two crucial factors involved in the proliferation and differentiation of B cells. Importantly, ZBTB24 exerts these functions independent of BCL-6 as it does not affect the expression and function of BCL-6. Our study thus not only provides a molecular explanation for the B-cell and antibody defects observed in ZBTB24-deficient ICF2 patients, but also indicates that ZBTB24 represents a novel transcriptional factor essentially involved in human B-cell functions.
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Simo-Riudalbas L, Diaz-Lagares A, Gatto S, Gagliardi M, Crujeiras AB, Matarazzo MR, Esteller M, Sandoval J. Genome-Wide DNA Methylation Analysis Identifies Novel Hypomethylated Non-Pericentromeric Genes with Potential Clinical Implications in ICF Syndrome. PLoS One 2015; 10:e0132517. [PMID: 26161907 PMCID: PMC4498748 DOI: 10.1371/journal.pone.0132517] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/15/2015] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION AND RESULTS Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are supposed to be expressed in germ line and silenced in somatic tissues. CONCLUSIONS In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients.
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Affiliation(s)
- L. Simo-Riudalbas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - A. Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - S. Gatto
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - M. Gagliardi
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - A. B. Crujeiras
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - M. R. Matarazzo
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - M. Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - J. Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
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Mikelsaar R, Paves H, Org K, Mikelsaar AV. Chromosome variant 1qh- and its influence on the 3D organization of chromosome 1 heterochromatin in interphase nucleus of patients with endometriosis. J Genet 2015; 93:219-23. [PMID: 24840844 DOI: 10.1007/s12041-014-0340-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ruth Mikelsaar
- Department of Human Biology and Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Street 19, Tartu 50411, Estonia.
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